galaxy-image-analysis/tools/cv2/cv2_extract_frames.xml at 37487fe2e1ecb360776305c92506c9a732a129b4 · rmassei/galaxy-image-analysis · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
<tool id="cv2_extract_frames" name="Extract video frames" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>with cv2</description>
    <macros>
        <token name="@TOOL_VERSION@">4.13.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@HELP_SECONDS@">Use a negative value to specify the time from the end of the video (e.g., a value of -1 corresponds to "1 second before the end of the video").</token>
        <import>tests.xml</import>
        <import>creators.xml</import>
    </macros>
    <creator>
        <expand macro="creators/rmassei"/>
    </creator>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="biii">opencv</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="4.13.0">opencv</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="cv2_extract_frames.py"/>
    </required_files>
    <command detect_errors="aggressive">
        <![CDATA[
        mkdir ./output_frames &&

        python '$__tool_directory__/cv2_extract_frames.py' output_frames
        -v '$video_path'
        -s '$start_time'
        #if str($end_time) != ""
            -e '$end_time'
        #end if
        -c '$convert_to_grey'

        && ls -l ./output_frames
        ]]>
    </command>
    <inputs>
        <param name="video_path" type="data" optional="False" format="mp4,avi" label="Input video to convert"/>
        <param name="start_time" type="float" value="0" optional="false" label="Start time"
               help="Start time in seconds. @HELP_SECONDS@"/>
        <param name="end_time" type="float" optional="true" label="End time"
               help="End time in seconds (optional). Leave empty to extract the sequence until the end of the video. @HELP_SECONDS@"/>
        <param name="convert_to_grey" type="boolean" label="Convert output to single-channel grayscale?"
               help="Convert the file to grayscale (will be RGB otherwise)."/>
    </inputs>
     <outputs>
        <collection name="frames" type="list" label="Output frames">
            <discover_datasets directory="output_frames" format="tiff" pattern="__name__"/>
        </collection>
    </outputs>
        <tests>
        <test>
            <!-- test MP4 w/o grayscale conversion -->
            <param name="video_path" value="input1.mp4"/>
            <param name="start_time" value="0"/>
            <param name="end_time" value="0.1"/>
            <param name="convert_to_grey" value="False"/>
            <output_collection name="frames" type="list">
                <expand macro="tests/intensity_image_diff/element" name="frame_0.tiff" value="frame_0.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="frame_1.tiff" value="frame_1.tiff" ftype="tiff"/>
            </output_collection>
        </test>
        <test>
            <!-- test MP4 w grayscale conversion -->
            <param name="video_path" value="input1.mp4"/>
            <param name="start_time" value="0"/>
            <param name="end_time" value="0.1"/>
            <param name="convert_to_grey" value="True"/>
            <output_collection name="frames" type="list">
                <expand macro="tests/intensity_image_diff/element" name="frame_2.tiff" value="frame_2.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="frame_3.tiff" value="frame_3.tiff" ftype="tiff"/>
            </output_collection>
        </test>
        <test>
            <!-- test AVI w/o grayscale conversion -->
            <param name="video_path" value="input2.avi"/>
            <param name="start_time" value="0"/>
            <param name="end_time" value="1"/>
            <param name="convert_to_grey" value="False"/>
            <output_collection name="frames" type="list">
                <expand macro="tests/intensity_image_diff/element" name="frame_4.tiff" value="frame_4.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="frame_5.tiff" value="frame_5.tiff" ftype="tiff"/>
            </output_collection>
        </test>
        <test>
            <!-- test AVI w grayscale conversion -->
            <param name="video_path" value="input2.avi"/>
            <param name="start_time" value="0"/>
            <param name="end_time" value="1"/>
            <param name="convert_to_grey" value="True"/>
            <output_collection name="frames" type="list">
                <expand macro="tests/intensity_image_diff/element" name="frame_6.tiff" value="frame_6.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="frame_7.tiff" value="frame_7.tiff" ftype="tiff"/>
            </output_collection>
        </test>
        <test>
            <!-- test AVI with endtime 0 -->
            <param name="video_path" value="input2.avi"/>
            <param name="start_time" value="0"/>
            <param name="end_time" value="0"/>
            <param name="convert_to_grey" value="True"/>
            <output_collection name="frames" type="list" count="1"/>
        </test>
        <test>
            <!-- test MP4 with endtime negative-->
            <param name="video_path" value="input1.mp4"/>
            <param name="start_time" value="0"/>
            <param name="end_time" value="-1"/>
            <param name="convert_to_grey" value="True"/>
            <output_collection name="frames" type="list" count="238"/>
        </test>
    </tests>
    <help>

        **Extract a sequence of image frames as TIFFs from MP4 and AVI files.**

        Frames captured within a specified time interval (in seconds) will be extracted from the video file as individual TIFF images.
        Optionally, the extracted frames can be converted to grayscale.

        **Codecs Support:**
        The tool was tested with H.264 and H.265 (HEVC) video codecs.
        The tool may support other codecs, though this has not been tested yet.
        If you have successfully converted files using alternative video formats or codecs, we would be grateful for your feedback at https://github.com/BMCV/galaxy-image-analysis.

    </help>
    <citations>
            <citation type="bibtex">@article{opencv_library,
            author = {Bradski, G.},
            citeulike-article-id = {2236121},
            journal = {Dr. Dobb's Journal of Software Tools},
            keywords = {bibtex-import},
            posted-at = {2008-01-15 19:21:54},
            priority = {4},
            title = {{The OpenCV Library}},
            year = {2000}
            }</citation>
    </citations>
</tool>